Analytical microarrays typically function as commercial analytical tools for research and other applications. Such tools study a wide variety of specific interactions and properties of molecular entities, most particularly nucleic acids, proteins, carbohydrates, lipids and a myriad of specifically or generically binding ligand molecules. Microarrays vary in overall size but are often on the order of 1 cm2 to 1 in2. The Microarray includes ordered and addressed positions, or cells, or features, each feature bearing physically attached, abundant copies of an identical probe entity. Rectangular arrays may range from as few as about 25 distinct features (as in 5×5) to as many as 2,500,000 distinct features (as in 1600×1600), with feature dimensions (diameter or square edge) ranging from 1 mm to 1 μm.
Typically, microarrays are fabricated or manufactured by manual or robotic depositions of probe entities to specified feature sites, or alternatively, the probe entities may be synthesized de novo, in parallel at specific feature sites of the array, using photochemical lithographic processes. Novel extensions or modifications of probes may also be used to adapt probe entities, taking advantage of unique or generic chemical or biochemical properties of the intermediate probe constructs.
Once assembled, a microarray represents a multiplex platform for analysis of specific and non-specific interactions with simple or complex mixtures of molecular targets that are brought into physical contact with the array, typically in a medium of surface-solution interface. Target entities may be generically or specifically labeled, as with fluorescent tags or intermediate binding elements such as biotin, before or after the interaction of target mixtures with fixed-probe arrays. Alternatively, site-specific interactions across the array may be monitored by target- or ligand-induced changes in labels associated with probe entities on the fixed array surface.
In the specific context of fluorescent labels, optical imaging provides the path for quantitative estimation of the extent of target-probe interaction, feature by feature across the array. Multiple fluorescent labels offer the opportunity to assess relative extents of interactions among different target entities at the same probe sites.
A notable variation on the rectangular microarray format and rationale is the application of suspended microspheres. In this configuration, each sphere is uniquely labeled with one or more fluorescent labels, and offers unique probe entities for interaction analysis on the sphere surface. As an example, the Luminex Corporation of Austin, Tex. offers such a suspended microsphere system.
Suspended multiplex mixtures of microspheres may be segregated by probes interacting with specific target entities bearing affinity markers for secondary binding to treated surface. Additionally, probes may segregate paramagnetic beads. As an example, the Invitrogen Corporation of Carlsbad, Calif. offers paramagnetic beads under the brand name Dynabeads®. Differentiation of beads isolated from mixtures is based upon fluorescence signature of dye labels embedded in the beads, by scanning beads settled onto an arrayed or random surface, or by direct flow cytometry of individual beads in suspension.
Fluorescent microarray image data acquisition is typically performed using mechanically and optically elaborate instrumentation with precise mechanical stage transport control and confocal epifluorescence measurements, for pixel by pixel sampling across the microarray field. Most often one or more lasers may be used to provide sufficient excitation illumination during the brief dwell time for photodetector measurement of fluorescence signal(s) at each pixel site. These systems are quite costly, typically on the order of $22 K-$180 K.
Such scanning detector systems are available for single arrays, or automated serial loading of multiple arrays for analysis, or for high throughput mechanical positioning of arrays of arrays in familiar microtiter trays—up to 96 microarrays per tray.
Presently, a simplified and more economical configuration is desired, devoid of the aforementioned limitations.